Valentina Di Francesco
The Institute for Systems Biology is using a systems biology approach to develop a detailed transcriptional network model of the interaction between the influenza virus and innate immune cells in vivo. This model will be integrated with comprehensive profiling of secreted proteins and eicosanoids in the influenza infected lung to construct a dynamic network model of the host response to the virus. In addition, they will examine how this network is perturbed by virulence factors that result in differential pathogenicity between influenza strains.
The program is using proteomic approaches to identify novel interactions between viral and host proteins and gain insight into host defense and viral evasion mechanisms. The lipid composition of both the viral envelope and the infected cell will be analyzed to establish whether these components influence the course of infection.
Studies will be extended to characterize the regulatory networks underlying the host response to secondary infection by S. aureus following a primary influenza infection. These studies will be complemented by systematically characterizing the transcriptional responses of S. aureus to the pulmonary environment of an influenza infected mouse.
Institute for Systems Biology (ISB)
Principal Investigator: Alan Aderem, Ph.D.
Co-Investigator: Ilya Shmulevich, Ph.D.
St. Jude Children’s Research Hospital
Co-Investigator: Peter Doherty, Ph.D.
Co-Investigator: Richard Webby, Ph.D
University of California, San Diego
Co-Investigator: Edward A. Dennis, Ph.D.
Seattle Children’s Hospital Research Institute
Co-Investigator: Craig Rubens, M.D., Ph.D.
Vanderbilt University, School of Medicine
Co-Investigator: H. Alex Brown, Ph.D.
In Focus 1, the program uses a systems biology approach to dissect the innate immune response to influenza infection in mice. This is accomplished through the following sub-aims: 1) In Vivo Regulatory Networks – The program aims to identify the regulatory networks in innate immune cells which control infection, and those which are subverted by highly pathogenic viruses. Transcriptional analysis of cells from the lungs of infected mice will provide the basis for this regulatory model. 2) Host Response; Secreted Proteins – The immune response to infection is, in large measure, coordinated by secreted proteins including cytokines and chemokines. The program will use proteomic techniques to comprehensively define the spectrum of proteins that are secreted into the airways throughout the infection. 3) Host Response; Secreted Lipids – Bioactive lipids, especially the eicosanoids, also control the innate immune response to infection and researchers will use mass spectrometry to identify the compendium of eicosonaoids generated in the lung in response to influenza infection. 4) In Vitro Regulatory Networks – As epithelial cells are the primary target for infection by the influenza virus, researchers will construct a detailed transcriptional regulatory model of influenza-infected primary epithelial cells, and identify those network interactions which correlate with virulence. 5) Finally, the program will examine how specific virulence elements present in highly pathogenic viruses perturb the host defense networks described in the previous sub-aims.
In this Research Focus the program will identify the host proteins that interact with influenza proteins and enumerate the lipid components of the influenza virion.
Viral-Host Protein Interactome – Proteomics methods will be utilized to generate a comprehensive protein-protein interaction map nucleated by select viral proteins throughout the natural infection cycle. The program perform quantitative proteomics to identify the host proteins bound by viral elements from strains of different pathogenicity.
Characterization of Viral Lipid Envelope – In this portion of the Research Focus the program aims to identify the constituent lipids of the strains of influenza under study; to determine changes in the lipid constituents of the host cells during infection, and to determine the relationship between the lipid composition of the viral envelope and the host cell from which it buds. The central hypothesis is that viral composition is in part defined by the identity of the host cell and the host cell composition is altered by the process of infection. The identification of the virus lipid composition will be analyzed with respect to its relative pathogenicity; in this way lipid composition may help to define essential parameters of viral function as well as identify selective targets for pharmacological intervention.
Superinfection involves mutual interactions between the host, virus, and bacteria. Transcriptome analysis on S. aureus as well as immune cells prior to and during bacterial challenge will reveal candidate genes and network mechanisms that are uniquely involved or enhanced in a superinfection.
Viral Strains - Several strains of varying pathogenicity have been developed for studying influenza in mice. The three strains described below provide an experimental system for comparing immune responses during lethal and sub-lethal influenza infections: 1) The H1N1 influenza virus A/Puerto Rico/34 (PR8) has been adapted to grow efficiently in the airways of mice, is lethal at relatively low doses, and is used widely as a model of influenza infection. 2) HKx31 (x31) is a reassortant virus that combines the surface HA and NA from an H3N2 virus (A/HK/x-31). In mice this virus serves as a non-lethal control that is similar to seasonal influenza in humans. 3) Researchers have developed a reassortant of PR8 and A/Vietnam/1203/2004, an H5N1 virus that was isolated from a fatal human infection in 2004.
Last Updated January 18, 2010